Michael Stanhope

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA
    Genome Biol Evol 2:646-55. 2010
  2. pmc Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution
    Haruo Suzuki
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
    Genome Biol Evol 3:168-85. 2011
  3. pmc Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 7:e37607. 2012
  4. pmc Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 14:920. 2013
  5. pmc Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 14:697. 2013
  6. pmc Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Microbiol 12:293. 2012
  7. pmc Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae
    Haruo Suzuki
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 13:38. 2012
  8. pmc Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Genome Biol 8:R71. 2007
  9. pmc Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread
    Michael J Stanhope
    Bioinformatics, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA
    Antimicrob Agents Chemother 49:4315-26. 2005
  10. doi request reprint Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development
    Michael J Stanhope
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Infect Genet Evol 8:331-9. 2008

Collaborators

Detail Information

Publications33

  1. pmc Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA
    Genome Biol Evol 2:646-55. 2010
    ....
  2. pmc Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution
    Haruo Suzuki
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
    Genome Biol Evol 3:168-85. 2011
    ....
  3. pmc Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
    PLoS ONE 7:e37607. 2012
    ..pyogenes adaptation to the human host was achieved in part by (i) the integration of new virulence factors (e.g. speB, and the sal locus) and (ii) the construction of new regulation networks (e.g. rgg, and to some extent speB)...
  4. pmc Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 14:920. 2013
    ..agalactiae growth and survival in the bovine mammary gland...
  5. pmc Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 14:697. 2013
    ..To address this deficit, we combined Roche-454 and Illumina sequencing technologies to characterize the first transciptome of any tissue for this species...
  6. pmc Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis
    Vincent P Richards
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Microbiol 12:293. 2012
    ..Streptococcus canis is an important opportunistic pathogen of dogs and cats that can also infect a wide range of additional mammals including cows where it can cause mastitis. It is also an emerging human pathogen...
  7. pmc Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae
    Haruo Suzuki
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    BMC Genomics 13:38. 2012
    ..aureus. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity...
  8. pmc Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Genome Biol 8:R71. 2007
    ..This study employs comparative evolutionary analyses of 26 Streptococcus genomes to yield an improved understanding of the relative roles of recombination and positive selection in pathogen adaptation to their hosts...
  9. pmc Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread
    Michael J Stanhope
    Bioinformatics, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA
    Antimicrob Agents Chemother 49:4315-26. 2005
    ..pneumoniae population density, such events could be an important means of resistance spread...
  10. doi request reprint Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development
    Michael J Stanhope
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Infect Genet Evol 8:331-9. 2008
    ..Our results suggest that clinical emphasis on TP domain sequences of these proteins may result in missing information relevant to antibiotic resistance development...
  11. ncbi request reprint The relative frequency of intraspecific lateral gene transfer of penicillin binding proteins 1a, 2b, and 2x, in amoxicillin resistant Streptococcus pneumoniae
    Michael J Stanhope
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
    Infect Genet Evol 7:520-34. 2007
    ..Although intraspecific LGT of pbps is occurring and has played a role in the spread of amoxicillin resistance in S. pneumoniae, clonal dissemination appears to be more significant...
  12. pmc Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens
    James R Brown
    Bioinformatics Division, GlaxoSmithKline, 1250 South Collegeville Road, UP1345, Collegeville, Pennsylvania 19426, USA
    EMBO Rep 4:692-8. 2003
    ..This study shows the importance of understanding complex evolutionary networks of ancient horizontal gene transfer for the development of novel antibiotics...
  13. doi request reprint Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray comparative genomic hybridization
    Ping Lang
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
    Infect Genet Evol 9:179-88. 2009
    ....
  14. pmc Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
    Tristan Lefebure
    Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
    Genome Res 19:1224-32. 2009
    ....
  15. ncbi request reprint Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV
    Michael J Stanhope
    Bioinformatics Division, Genetics Research, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
    Infect Genet Evol 4:15-9. 2004
    ..Our results are consistent with a hypothesis of viral host jumping events, concomitant with the reassortment of bird and mammalian coronaviruses, a scenario analogous to earlier outbreaks of influenzae...
  16. pmc Methods for data mining from large multinational surveillance studies
    James Poupard
    Antimicrobial Profiling and Clinical Microbiology, GlaxoSmithKline, 1250 S Collegeville Road, Mail Code UP1340, Collegeville, PA 19426 0989, USA
    Antimicrob Agents Chemother 46:2409-19. 2002
    ..As global surveillance studies become more common and new questions concerning the evolution of resistance are raised, innovative approaches to analysis of the data will increase in importance...
  17. pmc Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals subpopulations of Streptococcus pneumoniae with two distinct methionyl-tRNA synthetase genes
    Daniel R Gentry
    Department of Microbiology, Microbial, Musculoskeletal, and Proliferative Diseases Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania 19426, USA
    Antimicrob Agents Chemother 47:1784-9. 2003
    ..pneumoniae is the result of horizontal gene transfer which has been driven by selection for resistance to some unknown class of naturally occurring antibiotics with similarities to recently reported synthetic MetS inhibitors...
  18. pmc Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats
    Emma C Teeling
    Department of Biology, University of California, Riverside, CA 92521, USA
    Proc Natl Acad Sci U S A 99:1431-6. 2002
    ..An important implication of rhinolophoid polyphyly is independent evolution of key anatomical innovations associated with the nasal-emission of echolocation pulses...
  19. ncbi request reprint Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations
    Emmanuel J P Douzery
    Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, 34 095 Montpellier Cedex 05, France
    J Mol Evol 57:S201-13. 2003
    ..Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents...
  20. ncbi request reprint Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans
    Angela Burk-Herrick
    Biology Department, University of California, Riverside, 92521, USA
    Mamm Genome 17:257-70. 2006
    ..Our results demonstrate the necessity of including large numbers of sequences to elucidate functionally important sites of a protein when using a comparative evolutionary approach...
  21. ncbi request reprint Molecular evidence for the monophyly of tenrecidae (mammalia) and the timing of the colonization of Madagascar by Malagasy Tenrecs
    Christophe J Douady
    Biology and Biochemistry, Queen s University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, United Kingdom
    Mol Phylogenet Evol 22:357-63. 2002
    ..Molecular clock estimates suggest a split of otter shrews and Malagasy tenrecs at approximately 53 MYA. We estimate that the ancestor of Malagasy tenrecs dispersed to Madagascar subsequent to this split but prior to about 37 MYA...
  22. ncbi request reprint Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes
    Dorothee Huchon
    Laboratoire de Paléontologie, Paléobiologie et Phylogénie CC064, Institut des Sciences de l Evolution UMR 5554 CNRS, Universite Montpellier II, Place E Bataillon, Montpellier Cedex 05, France
    Mol Biol Evol 19:1053-65. 2002
    ..The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights...
  23. ncbi request reprint RbcL sequences indicate a single evolutionary origin of multinucleate cells in the red algal tribe Callithamnieae
    Lynne McIvor
    School of Biology and Biochemistry, Queen s University Belfast, Medical Biology Centre, 97 Lisburn Road, UK
    Mol Phylogenet Evol 23:433-46. 2002
    ..Multiple nuclei in each cell may combine the benefits of small C values (rapid cell cycle) with large cells (permitting morphological elaboration) while maintaining a constant ratio of nuclear volume: cytoplasmic volume...
  24. ncbi request reprint "Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis
    Christophe J Douady
    Dalhousie University, Department of Biochemistry and Molecular Biology, Halifax, Nova Scotia, Canada
    Mol Phylogenet Evol 30:778-88. 2004
    ..These results also highlight the potential pitfalls of single-gene and parsimony-only analyses...
  25. ncbi request reprint Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting
    Frédéric Delsuc
    Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, Montpellier, France
    Mol Biol Evol 19:1656-71. 2002
    ..By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling...
  26. ncbi request reprint Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews
    Christophe J Douady
    Queen s University of Belfast, Biology and Biochemistry, 97 Lisburn Road, Belfast, BT9 7BL, UK
    Mol Phylogenet Evol 25:200-9. 2002
    ..Our results provide convincing support for both lipotyphlan diphyly and the monophyly of Eulipotyphla. More surprisingly, we find strong evidence for a sister-group relationship between shrews and hedgehogs to the exclusion of moles...
  27. ncbi request reprint Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks
    Christophe J Douady
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5859 University Avenue, Halifax, Nova Scotia, Canada B3H 4H7
    Mol Phylogenet Evol 26:215-21. 2003
    ..Our phylogenetic placement of batoids as a basal elasmobranch lineage means that much of the current thinking regarding the evolution of morphological and life history characteristics in elasmobranchs needs to be re-evaluated...
  28. ncbi request reprint A retroposon analysis of Afrotherian phylogeny
    Hidenori Nishihara
    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
    Mol Biol Evol 22:1823-33. 2005
    ..Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed...
  29. pmc The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)
    Christophe J Douady
    Biology and Biochemistry, Queen s University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
    Proc Natl Acad Sci U S A 100:8325-30. 2003
    ....
  30. ncbi request reprint Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials
    Heather Amrine-Madsen
    Graduate Group in Genetics, University of California, Riverside 9252, USA
    Mol Phylogenet Evol 28:186-96. 2003
    ..Within Diprotodontia, both Vombatiformes and Phalangeriformes were supported at the 100% bootstrap level and with posterior probabilities of 1.00...
  31. ncbi request reprint Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes
    Frédéric Delsuc
    Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l Evolution, Universite Montpellier II, Montpellier, France
    Mol Phylogenet Evol 28:261-75. 2003
    ..However, low statistical support values associated with almost equal distributions of apomorphies among alternatives suggested that two parallel events of rapid speciation occurred within these two armadillo subfamilies...
  32. ncbi request reprint Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies
    Vincent P Richards
    National Coral Reef Institute, Oceanographic Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL 33004 USA
    Mol Ecol 16:139-57. 2007
    ..However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted...
  33. ncbi request reprint The use of composite taxa in supermatrices
    Mark S Springer
    Mol Phylogenet Evol 30:883-4. 2004

Research Grants3

  1. Evolutionary genomics and population genetics of pathogenic streptococci
    Michael Stanhope; Fiscal Year: 2009
    ..This information will in turn be a valuable asset to the development of novel therapeutic and preventative strategies for these pathogenic bacteria. ..
  2. Evolutionary genomics and population genetics of pathogenic streptococci
    Michael J Stanhope; Fiscal Year: 2010
    ..This information will in turn be a valuable asset to the development of novel therapeutic and preventative strategies for these pathogenic bacteria. ..